htsjdk.beta.plugin

Interface HtsDecoder<H extends HtsHeader,R extends HtsRecord>

Type Parameters:

H - type param for the header for this format (i.e. SAMFileHeader)

R - type param for the record for this format (i.e. SAMRecord)

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable, HtsQuery<R>, java.lang.Iterable<R>

All Known Subinterfaces:

HaploidReferenceDecoder, ReadsDecoder, VariantsDecoder

All Known Implementing Classes:

BAMDecoder, BAMDecoderV1_0, CRAMDecoder, CRAMDecoderV2_1, CRAMDecoderV3_0, FASTADecoderV1_0, HtsgetBAMDecoder, HtsgetBAMDecoderV1_2, SAMDecoder, SAMDecoderV1_0, VCFDecoder, VCFDecoderV3_2, VCFDecoderV3_3, VCFDecoderV4_0, VCFDecoderV4_1, VCFDecoderV4_2, VCFDecoderV4_3

public interface HtsDecoder<H extends HtsHeader,R extends HtsRecord>
extends HtsQuery<R>, java.io.Closeable

Base interface for decoders.

Implementations should not attempt to automatically resolve a companion index, and instead should only satisfy index queries when the provided input bundle explicitly specifies an index resource.

Method Summary

Modifier and Type	Method and Description
void	close() Close any resources associated with this decoder.
java.lang.String	getDisplayName() Get a user-friendly display name for this decoder.
java.lang.String	getFileFormat() Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).
H	getHeader() Get the file header for this decoder.
HtsVersion	getVersion() Get the version of the file format supported by this decoder.

Methods inherited from interface htsjdk.beta.plugin.interval.HtsQuery

hasIndex, isQueryable, iterator, query, query, query, query, queryContained, queryContained, queryContained, queryOverlapping, queryOverlapping, queryOverlapping, queryStart

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Method Detail

getFileFormat

java.lang.String getFileFormat()

Get the name of the file format supported by this decoder.The format name defines the underlying format handled by this decoder, and also corresponds to the format of the primary bundle resource that is required when decoding (see BundleResourceType and BundleResource.getFileFormat()).

Returns:

the name of the underlying file format handled by this decoder

getVersion

HtsVersion getVersion()

Get the version of the file format supported by this decoder.

getDisplayName

java.lang.String getDisplayName()

Get a user-friendly display name for this decoder.

Returns:

a user-friendly display name for this decoder for use in error and warning messages

getHeader

H getHeader()

Get the file header for this decoder.

Returns:

the file header for this decoder, of type H

close

void close()

Close any resources associated with this decoder.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable